Tools   Select Another Resource Report Type

http://amp.pharm.mssm.edu/Harmonizome/

Web application that allows for searching, visualization, and prediction about genes and proteins. It contains a collection of processed datasets gathered to serve and mine knowledge about genes and proteins from major online resources.

Proper citation: Harmonizome (RRID:SCR_016176) Copy   

•   Source: SciCrunch Registry

https://github.com/hakyimlab/PrediXcan

Software tool to detect known and novel genes associated with disease traits and provide insights into the mechanism of these associations. Used to test the molecular mechanisms through which genetic variation affects phenotype.

Proper citation: PrediXcan (RRID:SCR_016739) Copy   

•   Source: SciCrunch Registry

http://bioconductor.org/packages/release/bioc/html/ConsensusClusterPlus.html

Software written in R for determining cluster count and membership by stability evidence in unsupervised analysis. Provides quantitative and visual stability evidence for estimating the number of unsupervised classes in a dataset with item tracking, item consensus and cluster consensus plots.

Proper citation: ConsensusClusterPlus (RRID:SCR_016954) Copy   

•   Source: SciCrunch Registry

https://github.com/qiicr/dcmqi

Software library to help with the conversion between imaging research formats and the standard DICOM representation for image analysis results. Used to implement conversion of the data stored in commonly used research formats into the standard DICOM representation. Available as a precompiled binary package for every major operating system, as a Docker image, and as an extension to 3D Slicer.

Proper citation: dcmqi (RRID:SCR_016933) Copy   

•   Source: SciCrunch Registry

http://marrvel.org/

Web tool to search multiple public variant databases simultaneously and provide a unified interface to facilitate the search process. Used for integration of human and model organism genetic resources to facilitate functional annotation of the human genome. Used for analysis of human genes and variants by cross-disciplinary integration of records available in public databases to facilitate clinical diagnosis and basic research.

Proper citation: MARRVEL (RRID:SCR_016871) Copy   

•   Source: SciCrunch Registry

https://github.com/yarden/MISO/blob/fastmiso/docs/source/sashimi.rst

Software tool for quantitative visualization of aligned RNA-Seq reads that enables quantitative comparison of exon usage across samples or experimental conditions.

Proper citation: Sashimiplot (RRID:SCR_016861) Copy   

•   Source: SciCrunch Registry

https://github.com/BlaisProteomics/mzStudio

Software tool for proteomics data analysis, visualization, and notebook application. Dynamic digital canvas for user driven interrogation of mass spectrometry data. Operating system Unix/Linux, Windows.

Proper citation: mzStudio (RRID:SCR_017088) Copy   

•   Source: SciCrunch Registry

http://www.phosphosite.org

A freely accessible on-line systems biology resource devoted to all aspects of protein modification, as well as other post-translational modifications. It provides valuable and unique tools for both cell biologists and mass spectroscopists. PhosphoSite is a human- and mouse-centric database. It includes features such as: viewing the locations of modified residues on molecular models; browsing and searching MS2 records by disease, tissue, and cell line; submitting lists of peptides to identify previously reported genes; searching by sub-cellular localization, treatment, tissues, cell types, cell lines and diseases, and protein types and protein domains; searching for experimentally-verified kinase substrates and viewing preferred substrate motifs; and viewing MS2 spectra for peptides and sites not previously published.

Proper citation: PhosphoSitePlus: Protein Modification Site (RRID:SCR_001837) Copy   

•   Source: SciCrunch Registry

http://www.pathwaycommons.org/

Data management software that runs the Pathway Commons web service. It makes it easy to aggregate custom pathway data sets available in standard exchange formats from multiple databases, present pathway data to biologists via a customizable web interface, and export pathway data via a web service to third-party software, such as Cytoscape, for visualization and analysis. cPath is software only, and does not include new pathway information. Main features: * Import pipeline capable of aggregating pathway and interaction data sets from multiple sources, including: MINT, IntAct, HPRD, DIP, BioCyc, KEGG, PUMA2 and Reactome. * Import/Export support for the Proteomics Standards Initiative Molecular Interaction (PSI-MI) and the Biological Pathways Exchange (BioPAX) XML formats. * Data visualization and analysis via Cytoscape. * Simple HTTP URL based XML web service. * Complete software is freely available for local install. Easy to install and administer. * Partly funded by the U.S. National Cancer Institute, via the Cancer Biomedical Informatics Grid (caBIG) and aims to meet silver-level requirements for software interoperability and data exchange.

Proper citation: cPath (RRID:SCR_001749) Copy   

•   Source: SciCrunch Registry

https://david.ncifcrf.gov/

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025. Bioinformatics resource system including web server and web service for functional annotation and enrichment analyses of gene lists. Consists of comprehensive knowledgebase and set of functional analysis tools. Includes gene centered database integrating heterogeneous gene annotation resources to facilitate high throughput gene functional analysis.

Proper citation: DAVID (RRID:SCR_001881) Copy   

•   Source: SciCrunch Registry

https://bioconductor.org/packages/RAIDS/

Software R package to enable genetic ancestry inference from various cancer sequence sources (RNA, Exome, and Whole-Genome sequences). This package also implements simulation algorithm that generates synthetic cancer-derived data. Used for accurate and robust inference of genetic ancestry from cancer-derived molecular data across genomic platforms

Proper citation: RAIDS (Robust Ancestry Inference using Data Synthesis) (RRID:SCR_027265) Copy   

•   Source: SciCrunch Registry

https://github.com/JonathanIrish/MEMv3

Software tool to calculate enrichment scores. Generates human and machine readable labels that quantify features enriched in sample. Used to identify multiple populations of cells and to compare each population to all of other remaining cells from original sample.

Proper citation: Marker Enrichment Modeling (RRID:SCR_022495) Copy   

•   Source: SciCrunch Registry

https://cellrank.readthedocs.io/en/stable/

Software package for directed single cell fate mapping in diverse scenarios, including regeneration, reprogramming and disease. Automatically detects initial, intermediate and terminal populations, predicts fate potentials and visualizes continuous gene expression trends along individual lineages. Applied to lineage traced cellular reprogramming data, predicted fate probabilities correctly recover reprogramming outcomes.

Proper citation: CellRank (RRID:SCR_022827) Copy   

•   Source: SciCrunch Registry

https://mcmicro.org

Software tool as scalable, modular image processing pipeline for multiplexed tissue imaging. Transforms multi channel whole slide images into single cell data.

Proper citation: MCMICRO (RRID:SCR_022832) Copy   

•   Source: SciCrunch Registry

https://github.com/mhammell-laboratory/TEtranscripts

Software package for including transposable elements in differential enrichment analysis of sequencing datasets. Used for including transposable elements in differential expression analysis of RNA-seq datasets. RNAseq TE quantification tool.

Proper citation: TEtranscripts (RRID:SCR_023208) Copy   

•   Source: SciCrunch Registry

https://cibersort.stanford.edu/

Software tool to provide an estimation of the abundances of member cell types in a mixed cell population, using gene expression data. Used for characterizing cell composition of complex tissues from their gene expression profiles, large scale analysis of RNA mixtures for cellular biomarkers and therapeutic targets.

Proper citation: CIBERSORT (RRID:SCR_016955) Copy   

•   Source: SciCrunch Registry

https://sourceforge.net/projects/saint-apms/files/

Software tool for upgraded implementation of probabilistic scoring of affinity purification mass spectrometry data. Used for filtering high confidence interaction data from affinity purification mass spectrometry experiments. Used for assigning confidence scores to protein-protein interactions based on quantitative proteomics data in AP-MS experiments.

Proper citation: SAINTexpress (RRID:SCR_018562) Copy   

•   Source: SciCrunch Registry

https://seer.cancer.gov/siterecode/icdo3_dwhoheme/index.html

Website describing International Classification of Diseases-Oncology codes that corresponds to different cancer sites in the Surveillance, Epidemiology, and End Results (SEER) registry.

Proper citation: NCI Site Recode ICD-O-3/WHO 2008 Definition (RRID:SCR_024687) Copy   

•   Source: SciCrunch Registry

http://cabig.cancer.gov

THIS RESOURCE IS NO LONGER IN SERVICE, documented July 19, 2016. It has been integrated into the National Cancer Informatics Program (NCIP). The National Cancer Institute launched the cancer Biomedical Informatics Grid (caBIG) to create a virtual network of interconnected data, individuals, and organizations that worked together to redefine how cancer research is conducted. caBIG capabilities allowed researchers and clinicians to collaborate more effectively so that complex research questions might be asked and answered faster and more effectively. The mission of caBIG was to develop a truly collaborative information network that accelerated the discovery of new approaches for the detection, diagnosis, treatment, and prevention of cancer, ultimately improving patient outcomes.

Proper citation: Cancer Biomedical Informatics Grid (RRID:SCR_003328) Copy   

•   Source: SciCrunch Registry

https://github.com/JamieHeather/stitchr

Software Python tool for stitching coding T cell receptors nucleotide sequences from V,J,CDR3 information. Produces complete coding sequences representing fully spliced TCR cDNA given minimal V,J,CDR3 information.

Proper citation: Stitchr (RRID:SCR_022139) Copy   

•   Source: SciCrunch Registry